Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014554.1 Corchorus olitorius cultivar O-4 contig14587, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3604
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:898 original size:7 final size:7
Alignment explanation
Indices: 888--993 Score: 149
Period size: 7 Copynumber: 15.1 Consensus size: 7
878 GATCCATGAA
888 TTTTGAG
1 TTTTGAG
*
895 TTTTGAA
1 TTTTGAG
902 TTTTGAG
1 TTTTGAG
909 TTTTGAG
1 TTTTGAG
*
916 TTTTGAA
1 TTTTGAG
923 TTTTGAG
1 TTTTGAG
930 TTTTGAG
1 TTTTGAG
937 TTTTGAG
1 TTTTGAG
*
944 TTTTGAA
1 TTTTGAG
951 TTTTGAG
1 TTTTGAG
958 TTTTGAG
1 TTTTGAG
*
965 TTTTGAA
1 TTTTGAG
* *
972 TTTTAAA
1 TTTTGAG
*
979 TTTTGAA
1 TTTTGAG
986 TTTTGAG
1 TTTTGAG
993 T
1 T
994 AATGAAATGC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 89 1.00
ACGTcount: A:0.21, C:0.00, G:0.22, T:0.58
Consensus pattern (7 bp):
TTTTGAG
Found at i:1169 original size:33 final size:33
Alignment explanation
Indices: 1127--1200 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
1117 AGAAACTGTG
* * * *
1127 GATTTTGAACTTTGAGTTTTGATATGATATGTA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1160 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
1193 AATTTTGA
1 GATTTTGA
1201 CCTTCTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:1399 original size:54 final size:54
Alignment explanation
Indices: 1339--1567 Score: 336
Period size: 54 Copynumber: 4.2 Consensus size: 54
1329 CTAGATCACT
** * * * *
1339 TTAAGATCAACTTAGATTTTTGAAAA-CTTCTATGGAAGACCACACAGGGTCGTC
1 TTAAGATCAACTTAGACCTCT-AAAAGCTTCTATGAAAGACCACACTGGGTCATC
* * *
1393 TGAAGATCAACTTAGACTTCTAAAAGTTTCTATGAAAGACCACACTGGGTCATC
1 TTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
*
1447 TTAAGATCAACTTAGATCTCTGAAAA-CTTCTATGAAAGACCACACTGGGTCATC
1 TTAAGATCAACTTAGACCTCT-AAAAGCTTCTATGAAAGACCACACTGGGTCATC
1501 TTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
1 TTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
1555 TTAAGATCAACTT
1 TTAAGATCAACTT
1568 TCTAGAGAGA
Statistics
Matches: 160, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
53 8 0.05
54 148 0.93
55 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (54 bp):
TTAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
Found at i:1480 original size:108 final size:108
Alignment explanation
Indices: 1339--1567 Score: 386
Period size: 108 Copynumber: 2.1 Consensus size: 108
1329 CTAGATCACT
* * * *
1339 TTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAGGGTCGTCTGAAGATCAAC
1 TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAAGATCAAC
* *
1404 TTAGACTTCTAAAAGTTTCTATGAAAGACCACACTGGGTCATC
66 TTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
* *
1447 TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAAC
1 TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAAGATCAAC
1512 TTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
66 TTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
1555 TTAAGATCAACTT
1 TTAAGATCAACTT
1568 TCTAGAGAGA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 113 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (108 bp):
TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACAGGGTCATCTGAAGATCAAC
TTAGACCTCTAAAAGCTTCTATGAAAGACCACACTGGGTCATC
Found at i:1723 original size:37 final size:37
Alignment explanation
Indices: 1692--2166 Score: 447
Period size: 37 Copynumber: 12.8 Consensus size: 37
1682 AAACAAGTAC
* * *
1692 CTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* * * * * *
1729 TTTGAACAA-GATTTTGATGAGACACCTAAACAGGGAC
1 CTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGGAT
*
1766 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* * ** *
1803 CTAAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCAT
1 CTTAAATAAGGA-TTTGAT-AAGAAACCTAAACAGGGAT
1841 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* * * *
1878 CTTAAATAA-GATTTTGATGAGACACCTAAACGGGGAC
1 CTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGGAT
* * *
1915 CTTAAATAAGGATTTAATGAGAAACCTAAACAGGAAT
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* * * * * *
1952 CTTGAACAA-GATTTTGATGAGACATCTAAACAGGGAC
1 CTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGGAT
*
1989 CTTAAATAAGGATTTTGATAAGAAACCTAAACAGGAAT
1 CTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGGAT
* * * * * *
2027 CTTGAAA-AAAGTTTTGATGAGACACCTAAATAGGGAC
1 CTT-AAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* *
2064 CTTAAATAAGGATTTGATAAGAAATCTAAACAGGAAT
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
* * * * * * *
2101 CTTGAACAAGGTTTTGATGAGACACCTAGACAGGGAC
1 CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
*
2138 CTTAAATAAGGATTTGATAAGTAACCTAA
1 CTTAAATAAGGATTTGATAAGAAACCTAA
2167 TCAGAAATCT
Statistics
Matches: 347, Mismatches: 80, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
36 9 0.03
37 271 0.78
38 64 0.18
39 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
CTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
Found at i:1786 original size:74 final size:74
Alignment explanation
Indices: 1664--2197 Score: 748
Period size: 74 Copynumber: 7.2 Consensus size: 74
1654 CCTAAACTAG
* * * * * *
1664 GATTTTGAAGAGACAGCTAAACAAGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
*
1729 TTTGAACAA
66 CTTGAACAA
1738 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
**
1803 CTAAAACAAA
66 CTTGAAC-AA
* * * * * *
1813 AATTTTG-TCAAGAAACCTAAACAGGCATCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGA
1 GATTTTGAT-GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAA
* *
1877 TCTTAAATAA
65 TCTTGAACAA
* * *
1887 GATTTTGATGAGACACCTAAACGGGGACCTTAAATAAGGATTTAATGAGAAACCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
1952 CTTGAACAA
66 CTTGAACAA
*
1961 GATTTTGATGAGACATCTAAACAGGGACCTTAAATAAGGATTTTGATAAGAAACCTAAACAGGAA
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGAA
2026 TCTTGAA-AA
65 TCTTGAACAA
* * *
2035 AAGTTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAATCTAAACAGGAA
1 GA-TTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAA
2100 TCTTGAACAA
65 TCTTGAACAA
* * * * *
2110 GGTTTTGATGAGACACCTAGACAGGGACCTTAAATAAGGATTTGATAAGTAACCTAATCAGAAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
2175 CTTGAACAA
66 CTTGAACAA
*
2184 GGTTTTGATGAGAC
1 GATTTTGATGAGAC
2198 TGAATTTTGT
Statistics
Matches: 410, Mismatches: 44, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
74 278 0.68
75 132 0.32
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
CTTGAACAA
Found at i:1871 original size:149 final size:148
Alignment explanation
Indices: 1664--2197 Score: 748
Period size: 149 Copynumber: 3.6 Consensus size: 148
1654 CCTAAACTAG
* * * * * *
1664 GATTTTGAAGAGACAGCTAAACAAGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
*
1729 TTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
66 CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
**
1794 AACAGGAATCTAAAACAAA
131 AACAGGAATCTTGAAC-AA
* * * * * *
1813 AATTTTG-TCAAGAAACCTAAACAGGCATCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGA
1 GATTTTGAT-GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAA
* * * * *
1877 TCTTAAATAAGATTTTGATGAGACACCTAAACGGGGACCTTAAATAAGGATTTAATGAGAAACCT
65 TCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCT
1942 AAACAGGAATCTTGAACAA
130 AAACAGGAATCTTGAACAA
*
1961 GATTTTGATGAGACATCTAAACAGGGACCTTAAATAAGGATTTTGATAAGAAACCTAAACAGGAA
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGAA
* * *
2026 TCTTGAA-AAAAGTTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAATC
65 TCTTGAACAAGA-TTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
2090 TAAACAGGAATCTTGAACAA
129 TAAACAGGAATCTTGAACAA
* * * * *
2110 GGTTTTGATGAGACACCTAGACAGGGACCTTAAATAAGGATTTGATAAGTAACCTAATCAGAAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
*
2175 CTTGAACAAGGTTTTGATGAGAC
66 CTTGAACAAGATTTTGATGAGAC
2198 TGAATTTTGT
Statistics
Matches: 339, Mismatches: 41, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
148 77 0.23
149 262 0.77
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (148 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
AACAGGAATCTTGAACAA
Found at i:2056 original size:223 final size:223
Alignment explanation
Indices: 1664--2197 Score: 784
Period size: 223 Copynumber: 2.4 Consensus size: 223
1654 CCTAAACTAG
* * * * *
1664 GATTTTGAAGAGACAGCTAAACAAGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
*
1729 TTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
66 CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
*
1794 AACAGGAATCTAAAACAAAAATTTTGTCAAGAAACCTAAACAGGCATCTTAAATAAGGATTTGAT
131 AACAGGAATCTAAAACAAAAATTTTGTCAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGAT
* *
1859 AAGAAACCTAAACAGGGATCTTAAATAA
196 AAGAAACCTAAACAGGAATCTTAAACAA
* *
1887 GATTTTGATGAGACACCTAAACGGGGACCTTAAATAAGGATTTAATGAGAAACCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
*
1952 CTTGAACAAGATTTTGATGAGACATCTAAACAGGGACCTTAAATAAGGATTTTGATAAGAAACCT
66 CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAACCT
** * * * * *
2017 AAACAGGAATCTTGAA-AAAAGTTTTGAT-GAGACACCTAAATAGGGACCTTAAATAAGGATTTG
130 AAACAGGAATCTAAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCACCTTAAATAAGGATTTG
* *
2080 ATAAGAAATCTAAACAGGAATCTTGAACAA
194 ATAAGAAACCTAAACAGGAATCTTAAACAA
* * * * * *
2110 GGTTTTGATGAGACACCTAGACAGGGACCTTAAATAAGGATTTGATAAGTAACCTAATCAGAAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
*
2175 CTTGAACAAGGTTTTGATGAGAC
66 CTTGAACAAGATTTTGATGAGAC
2198 TGAATTTTGT
Statistics
Matches: 279, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
223 249 0.89
224 30 0.11
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (223 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTA
AACAGGAATCTAAAACAAAAATTTTGTCAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGAT
AAGAAACCTAAACAGGAATCTTAAACAA
Found at i:2634 original size:26 final size:26
Alignment explanation
Indices: 2576--2627 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2566 CCCCCCTTAT
2576 AATCCAAATTGACAACATTTGTCATC
1 AATCCAAATTGACAACATTTGTCATC
2602 AATCCAAATTGACAACATTTGTCATC
1 AATCCAAATTGACAACATTTGTCATC
2628 TTTCCAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (26 bp):
AATCCAAATTGACAACATTTGTCATC
Found at i:3166 original size:83 final size:83
Alignment explanation
Indices: 3007--3159 Score: 227
Period size: 83 Copynumber: 1.8 Consensus size: 83
2997 CAAACCTCCT
* *
3007 TCCAATTTGGTCATGCATTGATATTCCCAACTCAACTGATAGTTCTAGATCAGCTTCCCACCTTA
1 TCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATAGTTCTAGATCAACTTCCCACCTTA
3072 AGAAACTTTCAAGCATCC
66 AGAAACTTTCAAGCATCC
* * * * *
3090 TCCAATTTGATCATGCATTGATATTCCCAACTCAATTGAT-GTTTCTGGATCAATTTCTCATCTT
1 TCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATAG-TTCTAGATCAACTTCCCACCTT
3154 AAGAAA
65 AAGAAA
3160 TGTTCAAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 1 0.02
83 61 0.98
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (83 bp):
TCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATAGTTCTAGATCAACTTCCCACCTTA
AGAAACTTTCAAGCATCC
Found at i:3313 original size:4 final size:4
Alignment explanation
Indices: 3293--3370 Score: 56
Period size: 4 Copynumber: 19.8 Consensus size: 4
3283 TCCTTTTGAT
* *
3293 TTTC -TTC TTTA TTTC TTTC TTTC TTTC TTT- TTT- TTCAC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC
* * *
3338 TTTGC TTTC TCTTT TTTT TTTC TTTT TTTC TTT
1 TTT-C TTTC T-TTC TTTC TTTC TTTC TTTC TTT
3371 AGATTGCTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
3 11 0.18
4 40 0.67
5 9 0.15
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3338 original size:30 final size:30
Alignment explanation
Indices: 3299--3370 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
3289 TGATTTTCTT
3299 CTTTATTTCTTT-CTTTCT-TTCTTTTTTTTC
1 CTTT-TTTCTTTGCTTTCTCTT-TTTTTTTTC
3329 ACTTTTTTCTTTGCTTTCTCTTTTTTTTTTC
1 -CTTTTTTCTTTGCTTTCTCTTTTTTTTTTC
*
3360 TTTTTTTCTTT
1 CTTTTTTCTTT
3371 AGATTGCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
30 17 0.45
31 19 0.50
32 2 0.05
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (30 bp):
CTTTTTTCTTTGCTTTCTCTTTTTTTTTTC
Found at i:3339 original size:18 final size:18
Alignment explanation
Indices: 3311--3363 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3301 TTATTTCTTT
3311 CTTTCTTTCTTTTTTTTCA
1 CTTT-TTTCTTTTTTTTCA
** *
3330 CTTTTTTCTTTGCTTTCT
1 CTTTTTTCTTTTTTTTCA
3348 CTTTTTT-TTTTCTTTT
1 CTTTTTTCTTTT-TTTT
3364 TTTCTTTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.11
18 21 0.75
19 4 0.14
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
CTTTTTTCTTTTTTTTCA
Done.